Smoothly distributed fuzzy c-means: a new self-organizing map. - Roberto D. Pascual-Marqui; Alberto D. Pascual-Montano; Kieko Kochi; José María Carazo (Pattern Recognit., 2001)

Spin Images and Neural Networks for Efficient Content-Based Retrieval in 3D Object Databases. - Pedro A. de Alarcón; Alberto D. Pascual-Montano; José María Carazo (CIVR, 2002)

Modeling Shape and Topology of 3D Images of Biological Specimens. - Pedro A. de Alarcón; Alberto D. Pascual-Montano; Amarnath Gupta; José María Carazo (ICPR (1), 2002)

Engene: the processing and exploratory analysis of gene expression data. - Jorge García de la Nava; Daniel Franco Santaella; Jesús Cuenca Alba; José María Carazo; Oswaldo Trelles; Alberto D. Pascual-Montano (Bioinform., 2003)

Two-way clustering of gene expression profiles by sparse matrix factorization. - Alberto D. Pascual-Montano; Francisco Tirado; Pedro Carmona-Saez; José María Carazo; Roberto D. Pascual-Marqui (CSB Workshops, 2005)

A Speculative Parallel Algorithm for Self-Organizing Maps. - Carlos García 001; Manuel Prieto 001; Alberto D. Pascual-Montano (PARCO, 2005)

Optimization problems in electron microscopy of single particles. - Carlos Oscar Sánchez Sorzano; Roberto Marabini; Alberto D. Pascual-Montano; Sjors H. W. Scheres; José María Carazo (Ann. Oper. Res., 2006)

Integrated analysis of gene expression by association rules discovery. - Pedro Carmona-Saez; Monica Chagoyen; Andrés Rodríguez Moreno; Oswaldo Trelles; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

Biclustering of gene expression data by non-smooth non-negative matrix factorization. - Pedro Carmona-Saez; Roberto D. Pascual-Marqui; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

A literature-based similarity metric for biological processes. - Monica Chagoyen; Pedro Carmona-Saez; Concha Gil; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

Discovering semantic features in the literature: a foundation for building functional associations. - Monica Chagoyen; Pedro Carmona-Saez; Hagit Shatkay; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

bioNMF: a versatile tool for non-negative matrix factorization in biology. - Alberto D. Pascual-Montano; Pedro Carmona-Saez; Monica Chagoyen; Francisco Tirado; José María Carazo; Roberto D. Pascual-Marqui (BMC Bioinform., 2006)

Nonsmooth Nonnegative Matrix Factorization (nsNMF). - Alberto D. Pascual-Montano; José María Carazo; Kieko Kochi; Dietrich Lehmann; Roberto D. Pascual-Marqui (IEEE Trans. Pattern Anal. Mach. Intell., 2006)

CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem. - Mariana L. Neves; Monica Chagoyen; José María Carazo; Alberto D. Pascual-Montano (BioNLP, 2008)

Non-negative matrix factorization in bioinformatics: Towards understanding biological processes. - Alberto D. Pascual-Montano (ISCAS, 2008)

Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library. - Mariana L. Neves; José María Carazo; Alberto D. Pascual-Montano (BioLINK@ISMB/ECCB, 2008)

Named Entity Recognition and Normalization: A Domain-Specific Language Approach. - Miguel Vázquez; Monica Chagoyen; Alberto D. Pascual-Montano (IWPACBB, 2008)

ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. - Federico Abascal; Pedro Carmona-Saez; José María Carazo; Alberto D. Pascual-Montano (Bioinform., 2008)

Assessment of protein set coherence using functional annotations. - Monica Chagoyen; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2008)

bioNMF: a web-based tool for nonnegative matrix factorization in biology. - Edgardo Mejía-Roa; Pedro Carmona-Saez; Rubén Nogales; Cesar Vicente; Miguel Vázquez; X. Y. Yang; Carlos García 001; Francisco Tirado; Alberto D. Pascual-Montano (Nucleic Acids Res., 2008)

Extraction of biomedical events using case-based reasoning. - Mariana L. Neves; José María Carazo; Alberto D. Pascual-Montano (BioNLP@HLT-NAACL (Shared Task), 2009)

CentrosomeDB: a human centrosomal proteins database. - Rubén Nogales-Cadenas; Federico Abascal; Javier Díez-Pérez; José María Carazo; Alberto D. Pascual-Montano (Nucleic Acids Res., 2009)

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. - Rubén Nogales-Cadenas; Pedro Carmona-Saez; Miguel Vázquez; Cesar Vicente; Xiaoyuan Yang 001; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (Nucleic Acids Res., 2009)

SENT: semantic features in text. - Miguel Vázquez; Pedro Carmona-Saez; Rubén Nogales-Cadenas; Monica Chagoyen; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (Nucleic Acids Res., 2009)

Moara: a Java library for extracting and normalizing gene and protein mentions. - Mariana L. Neves; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2010)

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. - Ignacio Medina; José Carbonell; Luis Pulido; Sara C. Madeira; Stefan Götz 003; Ana Conesa; Joaquín Tárraga; Alberto D. Pascual-Montano; Rubén Nogales-Cadenas; Javier Santoyo; Francisco García-García 002; Martina Marbà; et al. (Nucleic Acids Res., 2010)

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. - Miguel Vázquez; Rubén Nogales-Cadenas; Javier Arroyo; Pedro Botías; Raul García; José María Carazo; Francisco Tirado; Alberto D. Pascual-Montano; Pedro Carmona-Saez (Nucleic Acids Res., 2010)

Finding closed frequent item sets by intersecting transactions. - Christian Borgelt; Xiaoyuan Yang 001; Rubén Nogales-Cadenas; Pedro Carmona-Saez; Alberto D. Pascual-Montano (EDBT, 2011)

Biclustering and classification analysis in gene expression using Nonnegative Matrix Factorization on multi-GPU systems. - Edgardo Mejía-Roa; Carlos García 001; José Ignacio Gómez; Manuel Prieto 001; Francisco Tirado; Rubén Nogales; Alberto D. Pascual-Montano (ISDA, 2011)

Parallelism on the Nonnegative Matrix Factorization. - Edgardo Mejía-Roa; Carlos García 001; José Ignacio Gómez; Manuel Prieto 001; Christian Tenllado; Alberto D. Pascual-Montano; Francisco Tirado (PARCO, 2011)

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. - Dietrich Rebholz-Schuhmann; Antonio Jimeno-Yepes; Chen Li 011; Senay Kafkas; Ian Lewin; Ning Kang 002; Peter T. Corbett; David Milward; Ekaterina Buyko; Elena Beisswanger; Kerstin Hornbostel; Alexandre Kouznetsov; et al. (J. Biomed. Semant., 2011)

U-Compare bio-event meta-service: compatible BioNLP event extraction services. - Yoshinobu Kano; Jari Björne; Filip Ginter; Tapio Salakoski; Ekaterina Buyko; Udo Hahn; K. Bretonnel Cohen; Karin Verspoor; Christophe Roeder; Lawrence E. Hunter; Halil Kilicoglu; Sabine Bergler; et al. (BMC Bioinform., 2011)

Gene expression modular analysis: an overview from the data mining perspective. - Alberto D. Pascual-Montano (WIREs Data Mining Knowl. Discov., 2011)

GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. - Daniel Tabas-Madrid; Rubén Nogales-Cadenas; Alberto D. Pascual-Montano (Nucleic Acids Res., 2012)

3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy. - Rubén Nogales-Cadenas; Slavica Jonic; Florence Tama; A. A. Arteni; Daniel Tabas-Madrid; Miguel Vázquez; Alberto D. Pascual-Montano; Carlos Oscar Sánchez Sorzano (Nucleic Acids Res., 2013)

A survey of dimensionality reduction techniques. - Carlos Oscar Sánchez Sorzano; Javier Vargas 001; Alberto Domingo Pascual-Montano (CoRR, 2014)

CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster. - Joao Miguel da Conceiçao Alves-Cruzeiro; Rubén Nogales-Cadenas; Alberto Domingo Pascual-Montano (Nucleic Acids Res., 2014)

NMF-mGPU: non-negative matrix factorization on multi-GPU systems. - Edgardo Mejía-Roa; Daniel Tabas-Madrid; Javier Setoain; Carlos García 001; Francisco Tirado; Alberto D. Pascual-Montano (BMC Bioinform., 2015)

NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning. - Javier Setoain; Mònica Franch; Marta Martínez; Daniel Tabas-Madrid; Carlos Oscar Sánchez Sorzano; Annette Bakker; Eduardo Gonzalez-Couto; Juan Elvira; Alberto D. Pascual-Montano (Nucleic Acids Res., 2015)